VCF/BCF: Annotation and analyis of next generation sequencing (NGS) data

VCF/BCF Documentation

Here is the documentation for VCF.

VCFsnippet

Tools for analyzing VCF/BCF data

R based tools: vcfR

Python based tools: PyVCF, cyvcf2

Linux based tools: bcftolls, github_bcftools, bioconda_bcftools

Analyze VCF file

samtools mpileup -f xxxxxx.fas -uv xxxxxx.sorted.bam > xxxxxx.vcf

number of entries for a particular chromosome

cat xxxxxx.vcf | grep -v “^##” | cut -f1 | grep -c “^Chr1”

cat xxxxxx.vcf | cut -f1 | grep " Chr1" | wc -l

number of adenines (A) in the file

cat xxxxxx.vcf | grep -v “^##” | cut -f4 | grep -P “^A$”

cat xxxxxx.vcf | cut -f4 | awk ‘$1 == “A”’ | wc -l

number of entries have exactly 20 supporting reads (read depth)

cat xxxxxx.vcf | grep -v “^##” | grep -c “DP=20;”

cat xxxxxx.vcf | cut -f8 | grep “DP=20” | wc -l

number of entries represent indels

cat xxxxxx.vcf | grep -v “^##” | grep -c INDEL

cat xxxxxx.vcf | cut -f8 | grep “INDEL” | wc -l (reduce the output by one)

number of entries on a specific chromosome and specific location (e.g., pos 175672 on Chr1)

cat xxxxxx.vcf | grep -v “^##” | cut -f1,2 | grep “Chr1” | grep 175672

cat xxxxxx.vcf | cut -f1,2 | grep “Chr1” | awk ‘$2 == “175672”’ | wc -l

Analyze compressed VCF (VCF.gz) file

samtools mpileup -f xxxxxx.fas -g xxxxxx.sorted.bam > xxxxxx.bcf

all reported variants on chromosome 3

zcat xxxxxx.vcf.gz | cut -f1 | grep “Chr3” | wc -l

number of A to T mutations in a tabular fashion (-P for pattern,‘t’ for tabular)

zcat xxxxxx.vcf.gz | cut -f4,5 | awk ‘$1 == “A” && $2 == “T”’ | wc -l

number of indels in the file

zcat xxxxxx.vcf.gz | cut -f8 | grep “INDEL” | wc -l

finding the type of mutation at a particular position in a particular chromosome

zcat xxxxxx.vcf.gz |grep “Chr3”|awk ‘$2==“11937923”’|head

number of entries have precisely 20 supporting reads (read depth)

zcat xxxxxx.vcf.gz | cut -f8 | grep “DP=20” | wc -l

Convert BCF to VCF for analysis

call variants using ‘BCFtools call’ with the multi-allelic caller (option ‘-m’), showing only variant sites (‘-v’) and presenting the output in uncompressed VCF format (‘-O v’)

bcftools call -m -v -O v xxxxxx.bcf > xxxxxx.vcf

all reported variants on chromosome 3

cat xxxxxx.vcf | grep -v “^##” | cut -f1 | sort | uniq -c | grep “Chr3”

number of A to T mutations in a tabular fashion (-P for pattern,‘t’ for tabular)

cat xxxxxx.vcf | grep -v “^##” | cut -f4,5 | grep -P “^A$” | wc -l

number of indels

cat xxxxxx.vcf | cut -f8 | grep “INDEL” | wc -l